MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iLB1027_lipid [2].
Target metabolite : pi_m
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 31: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: PHATRDRAFT_45947 PHATRDRAFT_54477 PHATRDRAFT_12762 Phatr3_EG02232 PHATRDRAFT_26290 PHATRDRAFT_55126 PHATRDRAFT_36256 PHATRDRAFT_49339 PHATRDRAFT_29157 PHATRDRAFT_32747 PHATRDRAFT_25308 PHATRDRAFT_22357 PHATRDRAFT_7164 PHATRDRAFT_45846 PHATRDRAFT_36048 PHATRDRAFT_51703 PHATRDRAFT_draft462 PHATRDRAFT_46692 PHATRDRAFT_17265 Phatr3_EG02569 PHATRDRAFT_21970 PHATRDRAFT_31436 PHATRDRAFT_32849 PHATRDRAFT_draft1517 PHATRDRAFT_28585 PHATRDRAFT_43697   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359607 (mmol/gDw/h)
  Minimum Production Rate : 0.005634 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_photon_e : 544.093990
  EX_co2_e : 22.030553
  EX_h2o_e : 17.659767
  EX_no3_e : 1.760000
  EX_pi_e : 0.220000
  EX_so4_e : 0.135840
  EX_mg2_e : 0.006427

Product: (mmol/gDw/h)
  EX_o2_e : 26.257349
  SK_for_c : 4.589259
  EX_h_e : 2.521532
  DM_biomass_c : 0.359607
  Auxiliary production reaction : 0.130707
  DM_dmsp_c : 0.071888

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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